Baking a normal map on to two (seemingly) identical cubes is producing different results
The two lowres cubes are not the same. You may have rotated them or changed the vertices in Edit mode somehow... Here are the vertices IDs shown using the MeasureIt Addon (also possible by enabling developer mode in settings somehow). 



Also the UV unwrap are not the same either for probably the same reason. If you split the seemingly same quad face into two triangles, they appear at different positions in the UV, meaning the quad faces are in different orientations to begin with.




Finally, simply duplicating the first lowres and baking the texture with the dup produces the same result as its source. 



In essence, you have to add proper UV's to your low-res geometry to avoid artefacts and you have to make sure that the dimensions of both geometries are roughly the same, then it will bake fine: